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[bioontology-support] ATC / bioportal

Alexander Garcia Castro alexgarciac at gmail.com
Tue Jan 10 12:23:12 PST 2017


could the difference be due to the transformation from the ATC original
format to the  UMLS format?

On Tue, Jan 10, 2017 at 3:13 PM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hello Olga,
>
>
> On Jan 9, 2017, at 8:38 PM, Olga Ximena Giraldo <oxgiraldo at gmail.com>
> wrote:
>
> If I understand correctly you do not take care of converting
> (transforming) the original WHO ATC vocabulary into an RDF file. Instead,
> you just take whatever UMLS has and that is what you transform to RDF.
> Right?
>
>
>
> Yes, that’s correct.
>
>
>
> The original WHO ATC, as available at [1]  does not have the classes
> “Ergot alkaloid oxytocics” and “Porstaglandins, Oxytocics”
>
> while the one in bioportal does have these two classes [2], [3].
>
>
>
> You are seeing those classes because they are present in the UMLS
> distribution of ATC that we imported into BioPortal (UMLS version 2016AA).
> I’ve included a couple of screenshots below from the UMLS Metathesaurus
> Browser where you can execute searches restricted by source ontology and
> release version.
>
>
>
>
> I would like to know what other differences in the hierarchy are there
> between the original WHO ATC (14 main groups) and that in bioportal (17
> main groups) [4].
>
>
>
> The version of ATC contained in the UMLS has 17 root classes - that’s why
> you see the same in BioPortal (another screenshot below of the ATC
> hierarchy from the UMLS Browser).  We don’t modify the contents of the
> ontology when we do the import.
>
> I’m assuming the website you mention below (https://www.whocc.no/atc_ddd_
> index/) offers the most current version of ATC (although I didn’t see a
> version number anywhere)?  If you’re seeing differences between the
> canonical distribution from the WHO and BioPortal content, it’s likely
> because BioPortal has an older version.  According to UMLS documentation,
> ATC is only updated in their system once annually:
>
> https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ATC/
> index.html
>
> Kind regards,
> Jennifer
>
>
> thanks in advance,
>
>
> [1] https://www.whocc.no/atc_ddd_index/
>
> [2] http://bioportal.bioontology.org/ontologies/ATC/?p=classes&
> conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FUATC%2FG02AB
>
> [3] http://bioportal.bioontology.org/ontologies/
> ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%
> 2Fontology%2FUATC%2FG02AD
>
> [4] http://bioportal.bioontology.org/ontologies/ATC?p=classes&
> conceptid=root
>
>
>
>
>
>
>
>
>
>
>
>
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> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>


-- 
Alexander Garcia
http://www.alexandergarcia.name/
http://www.usefilm.com/photographer/75943.html
http://www.linkedin.com/in/alexgarciac
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